In the coastal Japanese city of Gensouto, Ordinary High-School Student Koishi Komeiji has been living alone for the last few months (apart from her pet cat and raven) since her sister Satori vanished without a trace. Bullied and lonely, when she hears a rumour about an abandoned shrine that grants wishes, she begs for someone strong and brave to look after her. Instead a strange jewel materialises out of thin air, and she's attacked by Fish People only to be saved by a talking dolphin. The dolphin tells Koishi to squeeze the jewel, and she defeats the fishmen by transforming into the "Siren" Dolphin Rider Koishi. Back at her apartment the now-human dolphin explains that she is a youkai, and a junior member of a human-protecting organisation called the Order of the White Pearl. Koishi and the dolphin (named Sango) must find the remaining six Sirens before the White Pearl's enemies, the Children of the Black Claw, can use their powers for evil.

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A Day in the Limelight: While most of the Windows and PC-98 cast appear to exist in some form, the protagonist is Koishi, who has never been a playable character (in the main games, at least). Reimu only appears as a minor character, and Marisa has only been mentioned in a single line of throwaway dialogue.

Hoist by His Own Petard: The Ravager was created by the Kappa to defeat the humans in the war, and succeeded with flying colors. Then it started attacking youkai, and nearly caused the extinction of life on Earth, because it just liked killing.

How Do I Shot Web?: Sakuya and Komachi (and possibly Koishi) were initially using their powers subconsciously, unaware that they had them.

Humans Are Average: Humans' magic powers are generally weaker than those of youkai, but far more varied.

Humans Are Flawed, if not Bastards: The Black Claw believe firmly in the latter, and not even everyone in the Pearl is especially keen on humans. Koishi believes in the former, with the added clause that "flawed" does not mean "evil." This is also a big reason behind Satori's FaceHeel Turn.

Laser-Guided Amnesia: Curing the victim of a Mindcoil leaves them with only a general recollection of their actions, erasing any information on magic. Seeing the Sirens fight the rebellious youkai in the zoo jogs their memory, though, as we see with Cirno and Yuyuko. The White Pearl can also create this effect on purpose.

Rank Inflation: Nitori has a confusing set of power ranks for magic-users which includes "B", "S+" and "XS+++".

The Reveal: A few pretty big ones: The Masked Woman being Satori, Iku being Leviathan, Aptera needing magical power from either humans or youkai...

Rousseau Was Right: Koishi believes that humans aren't monsters, but rather that circumstances beyond their control sometimes drive them to do terrible things. The story goes to great lengths to illustrate that idea, and the finale, which has humans and youkai living peacefully again, further drives her point home.

Sadistic Choice: The blade Aptera was created by Yukari to destroy the Ravager, but requires an entire race's worth of magic to use. Draining either the magic of all humans or all youkai would seemingly lead to disaster in either case. Koishi works out how to Take a Third Option.

Un-Paused: When Ran visits the Komeiji house to warn of Mamizou's attack on the zoo, Sango, thinking her to be malicious, runs up to attack her, leading Ran to put a stasis field around her so she can talk to Koishi peacefully. Once she leaves, she gets rid of the field, causing Sango to hit nothing and run face-first into a wall.

"Koishi-san, let me get this straight. You humans have invented a system that lets you cut spare keys to any door. No fuss, no pizazz, no evidence. Youre telling me that youd rather I had to go through a lockpicking charm every time I wanted to get in here after hours? Jeez, and you say that Im crazy."

Villainous Breakdown: Pretty much all of the Mindcoil victims when they're about to be defeated. The Ravager as well, once the Sirens start doing to real damage to it.

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